Problem installing the latest version #4146

cwangaw · 2025-03-24T06:31:17Z

cwangaw
Mar 24, 2025

Hi all,

I had the previous version installed correctly. However, since it kept refining the boundary elements in 3D adaptive meshes, I had to update to the latest version. And I failed to install it correctly. Attached are the log files for building PETSc: make.log, configure.log.

For the firedrake part, I cannot find an installation log file in my directory.

To summarize the problem, for the PETSc part, everything went well until the check part.

$ make PETSC_DIR=/home/wan01937/Workspace/petsc PETSC_ARCH=arch-firedrake-default check
Running PETSc check examples to verify correct installation
Using PETSC_DIR=/home/wan01937/Workspace/petsc and PETSC_ARCH=arch-firedrake-default
Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
See https://petsc.org/release/faq/
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
Number of SNES iterations = 2
Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes
See https://petsc.org/release/faq/
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
Number of SNES iterations = 2
0a1,4
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
3,4c7,8
<   1 SNES Function norm 4.12227e-06
<   2 SNES Function norm 6.098e-11
---
>   1 SNES Function norm 3.32882e-06
>   2 SNES Function norm < 1.e-11
/home/wan01937/Workspace/petsc/src/snes/tutorials
Possible problem with ex19 running with HYPRE, diffs above
=========================================
0a1,4
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
/home/wan01937/Workspace/petsc/src/snes/tutorials
Possible problem with ex19 running with MUMPS, diffs above
=========================================
0a1,3
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
/home/wan01937/Workspace/petsc/src/snes/tutorials
Possible problem with ex19 running with SuiteSparse, diffs above
=========================================
0a1,3
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
/home/wan01937/Workspace/petsc/src/snes/tutorials
Possible problem with ex19 running with SuperLU_DIST, diffs above
=========================================
0a1,3
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
> Invalid MIT-MAGIC-COOKIE-1 key
/home/wan01937/Workspace/petsc/src/vec/vec/tests
Possible problem with ex47 running with HDF5, diffs above
=========================================
Completed PETSc check examples
Error while running make check
gmake[1]: *** [makefile:131: check] Error 1
make: *** [GNUmakefile:17: check] Error 2

I tried to ignore it and continue to building the firedrake. However, it did not work.

wan01937@vh512-2:~/Workspace$ python3 -m venv venv-firedrake
wan01937@vh512-2:~/Workspace$ . venv-firedrake/bin/activate
(venv-firedrake) wan01937@vh512-2:~/Workspace$ export $(python3 firedrake-configure --show-env)
(venv-firedrake) wan01937@vh512-2:~/Workspace$ pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git#[test]"
Collecting firedrake@ git+https://github.com/firedrakeproject/firedrake.git#[test] (from firedrake@ git+https://github.com/firedrakeproject/firedrake.git#[test])
  Cloning https://github.com/firedrakeproject/firedrake.git to /tmp/pip-install-6361a1in/firedrake_a874eb92ed384427b90acfe519935cc4
  Running command git clone --filter=blob:none --quiet https://github.com/firedrakeproject/firedrake.git /tmp/pip-install-6361a1in/firedrake_a874eb92ed384427b90acfe519935cc4
  Resolved https://github.com/firedrakeproject/firedrake.git to commit a041b2a088b46d849b33ef6b249df124035a016a
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
 
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [19 lines of output]
      Traceback (most recent call last):
        File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-uasg_y4e/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-uasg_y4e/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-uasg_y4e/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 102, in <module>
        File "<string>", line 39, in get_petsc_variables
      FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pip-build-env-6emx6nn4/normal/lib/python3.12/site-packages/petsc/lib/petsc/conf/petscvariables'
      [end of output]
 
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Answered by cwangaw

Mar 25, 2025

I finally made it work by installing SLEPc similar to the way of installing PETSc, and then install slepc4py by pip after installing the firedrake.

However, I got segmentation fault by msh = msh.refine_marked_elements(mark) with the error message

[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0…

View full answer

connorjward · 2025-03-24T09:19:56Z

connorjward
Mar 24, 2025
Maintainer

What operating system (and version) are you using?

The "invalid MIT-MAGIC" error looks to be some sort of error with X forwarding or something. A quick search found this which may be helpful.

Regarding the last part of the issue. Did you run pip cache remove petsc4py?

16 replies

cwangaw Mar 24, 2025
Author

I see. Thanks!

When I try echo $SLEPC_DIR, it shows nothing. But when I try pip install slepc, I am told that it is already installed:

Requirement already satisfied: slepc in /home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages (3.22.2)
Requirement already satisfied: petsc<3.23,>=3.22 in /home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages (from slepc) (3.22.4)
Requirement already satisfied: mpi4py>=1.2.2 in /home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages (from petsc<3.23,>=3.22->slepc) (4.0.3)

But if I set it by export SLEPC_DIR=/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/slepc, the program still cannot find the slepc showing ImportError: libslepc.so.3.22: cannot open shared object file: No such file or directory. Although I can clearly see that I have the file with this name in the directory /home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/slepc/lib/libslepc.so.3.22.

connorjward Mar 24, 2025
Maintainer

Can you reinstall slepc4py having first cleared the cache and exported SLEPC_DIR?

cwangaw Mar 24, 2025
Author

It shows a different error message now. But I'm not sure if I am understanding correctly. I did

pip uninstall slepc4py
pip cache remove slepc4py
export SLEPC_DIR=/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/slepc
pip install slepc4py

And here is what I got:

(venv-firedrake) wan01937@vh512-2:~/Workspace/GaN/fd_mpi$ pip cache remove slepc4py
WARNING: No matching packages for pattern "slepc4py"
Files removed: 0
(venv-firedrake) wan01937@vh512-2:~/Workspace/GaN/fd_mpi$ export SLEPC_DIR=/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/slepc
(venv-firedrake) wan01937@vh512-2:~/Workspace/GaN/fd_mpi$ pip install slepc4py
Collecting slepc4py
  Using cached slepc4py-3.22.2.tar.gz (137 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.19 in /home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages (from slepc4py) (2.2.4)
Requirement already satisfied: petsc<3.23,>=3.22 in /home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages (from slepc4py) (3.22.4)
Requirement already satisfied: petsc4py<3.23,>=3.22 in /home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages (from slepc4py) (3.22.4)
Requirement already satisfied: mpi4py>=1.2.2 in /home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages (from petsc<3.23,>=3.22->slepc4py) (4.0.3)
Building wheels for collected packages: slepc4py
  Building wheel for slepc4py (pyproject.toml) ... done
  Created wheel for slepc4py: filename=slepc4py-3.22.2-cp312-cp312-linux_x86_64.whl size=2385522 sha256=02bef3b932451e6980c5a6ec13485b9c8e5810fb32ff6c92da47f9cb3311d8c9
  Stored in directory: /home/wan01937/.cache/pip/wheels/9b/55/e9/9e82084c37f7feaeacdb68ad7d3d635f2b254ae675bfe61c08
Successfully built slepc4py
Installing collected packages: slepc4py
Successfully installed slepc4py-3.22.2
(venv-firedrake) wan01937@vh512-2:~/Workspace/GaN/fd_mpi$ python3 solvers.py
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Traceback (most recent call last):
  File "/home/wan01937/Workspace/GaN/fd_mpi/solvers.py", line 6, in <module>
    from utilities import *
  File "/home/wan01937/Workspace/GaN/fd_mpi/utilities.py", line 1, in <module>
    from firedrake import * 
    ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/firedrake/__init__.py", line 70, in <module>
    from firedrake.eigensolver import *
  File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/firedrake/eigensolver.py", line 11, in <module>
    from slepc4py import SLEPc
  File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/slepc4py/SLEPc.py", line 4, in <module>
    SLEPc = ImportSLEPc(ARCH)
            ^^^^^^^^^^^^^^^^^
  File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/slepc4py/lib/__init__.py", line 32, in ImportSLEPc
    path, arch = getPathArchSLEPc(arch)
                 ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/slepc4py/lib/__init__.py", line 47, in getPathArchSLEPc
    path, arch = getPathArch(path, arch, rcvar, rcfile)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wan01937/Workspace/venv-firedrake/lib/python3.12/site-packages/petsc4py/lib/__init__.py", line 122, in getPathArch
    raise TypeError("invalid arch value: '%s'" % arch)
TypeError: invalid arch value: 'arch-firedrake-default'

cwangaw Mar 25, 2025
Author

I finally made it work by installing SLEPc similar to the way of installing PETSc, and then install slepc4py by pip after installing the firedrake.

However, I got segmentation fault by msh = msh.refine_marked_elements(mark) with the error message

[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 59.

But the exact code actually worked for the previous version of firedrake. (Unfortunately, I have deleted that.)

I found that may because I had periodic boundary conditions. When I construct the geometry by removing the periodicity of the geometry, everything works well.

I think this is not an installation problem. So I will open another thread to ask about it.

Thank you so much for all your help!!!

Answer selected by connorjward

connorjward Mar 25, 2025
Maintainer

OK. Glad this works at least!

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Problem installing the latest version #4146

cwangaw Mar 24, 2025

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connorjward Mar 24, 2025 Maintainer

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